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Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapōlā'au and the Hawai'i 'amakihi.

Campana MG, Corvelo A, Shelton J, Callicrate TE, Bunting KL, Riley-Gillis B, Wos F, DeGrazia J, Jarvis ED, Fleischer RC.

J Hered. 2020 Feb 5;111(1):21-32. doi: 10.1093/jhered/esz057.


Evolution of vocal learning and spoken language.

Jarvis ED.

Science. 2019 Oct 4;366(6461):50-54. doi: 10.1126/science.aax0287. Epub 2019 Oct 3. Review.


Identification and characterization of primordial germ cells in a vocal learning Neoaves species, the zebra finch.

Jung KM, Kim YM, Keyte AL, Biegler MT, Rengaraj D, Lee HJ, Mello CV, Velho TAF, Fedrigo O, Haase B, Jarvis ED, Han JY.

FASEB J. 2019 Dec;33(12):13825-13836. doi: 10.1096/fj.201900760RR. Epub 2019 Oct 11.


Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype.

Borges R, Fonseca J, Gomes C, Johnson WE, O'Brien SJ, Zhang G, Gilbert MTP, Jarvis ED, Antunes A.

Genome Biol Evol. 2019 Aug 1;11(8):2244-2255. doi: 10.1093/gbe/evz111.


Parrot Genomes and the Evolution of Heightened Longevity and Cognition.

Wirthlin M, Lima NCB, Guedes RLM, Soares AER, Almeida LGP, Cavaleiro NP, Loss de Morais G, Chaves AV, Howard JT, Teixeira MM, Schneider PN, Santos FR, Schatz MC, Felipe MS, Miyaki CY, Aleixo A, Schneider MPC, Jarvis ED, Vasconcelos ATR, Prosdocimi F, Mello CV.

Curr Biol. 2018 Dec 17;28(24):4001-4008.e7. doi: 10.1016/j.cub.2018.10.050. Epub 2018 Dec 6.


Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.


Divergence in problem-solving skills is associated with differential expression of glutamate receptors in wild finches.

Audet JN, Kayello L, Ducatez S, Perillo S, Cauchard L, Howard JT, O'Connell LA, Jarvis ED, Lefebvre L.

Sci Adv. 2018 Mar 14;4(3):eaao6369. doi: 10.1126/sciadv.aao6369. eCollection 2018 Mar.


De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.

Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED.

Gigascience. 2017 Oct 1;6(10):1-16. doi: 10.1093/gigascience/gix085.


A hypothesis on a role of oxytocin in the social mechanisms of speech and vocal learning.

Theofanopoulou C, Boeckx C, Jarvis ED.

Proc Biol Sci. 2017 Aug 30;284(1861). pii: 20170988. doi: 10.1098/rspb.2017.0988. Review.


Axon guidance pathways served as common targets for human speech/language evolution and related disorders.

Lei H, Yan Z, Sun X, Zhang Y, Wang J, Ma C, Xu Q, Wang R, Jarvis ED, Sun Z.

Brain Lang. 2017 Nov;174:1-8. doi: 10.1016/j.bandl.2017.06.007. Epub 2017 Jul 8.


Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs.

Chabout J, Jones-Macopson J, Jarvis ED.

J Vis Exp. 2017 May 9;(123). doi: 10.3791/54137.


Overexpression of human NR2B receptor subunit in LMAN causes stuttering and song sequence changes in adult zebra finches.

Chakraborty M, Chen LF, Fridel EE, Klein ME, Senft RA, Sarkar A, Jarvis ED.

Sci Rep. 2017 Apr 21;7(1):942. doi: 10.1038/s41598-017-00519-8.


A Foxp2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice.

Chabout J, Sarkar A, Patel SR, Radden T, Dunson DB, Fisher SE, Jarvis ED.

Front Behav Neurosci. 2016 Oct 20;10:197. eCollection 2016.


Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.

Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM.

Genome Biol Evol. 2016 Aug 25;8(8):2442-51. doi: 10.1093/gbe/evw166.


Bone-associated gene evolution and the origin of flight in birds.

Machado JP, Johnson WE, Gilbert MT, Zhang G, Jarvis ED, O'Brien SJ, Antunes A.

BMC Genomics. 2016 May 18;17:371. doi: 10.1186/s12864-016-2681-7.


Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds.

Almeida D, Maldonado E, Khan I, Silva L, Gilbert MT, Zhang G, Jarvis ED, O'Brien SJ, Johnson WE, Antunes A.

Genome Biol Evol. 2016 Apr 13;8(4):1115-31. doi: 10.1093/gbe/evw041.


Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

Jarvis ED.

Annu Rev Anim Biosci. 2016;4:45-59. doi: 10.1146/annurev-animal-021815-111216. Review.


Brain evolution by brain pathway duplication.

Chakraborty M, Jarvis ED.

Philos Trans R Soc Lond B Biol Sci. 2015 Dec 19;370(1684). pii: 20150056. doi: 10.1098/rstb.2015.0056. Review.


Surviving as an underrepresented minority scientist in a majority environment.

Jarvis ED.

Mol Biol Cell. 2015 Nov 1;26(21):3692-6. doi: 10.1091/mbc.E15-06-0451.


Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Haug-Baltzell A, Jarvis ED, McCarthy FM, Lyons E.

Front Neurosci. 2015 Oct 7;9:361. doi: 10.3389/fnins.2015.00361. eCollection 2015.


Listening in.

Jarvis ED.

Elife. 2015 Oct 21;4:e11665. doi: 10.7554/eLife.11665.


The Origin and Diversification of Birds.

Brusatte SL, O'Connor JK, Jarvis ED.

Curr Biol. 2015 Oct 5;25(19):R888-98. doi: 10.1016/j.cub.2015.08.003. Review.


Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Borges R, Khan I, Johnson WE, Gilbert MT, Zhang G, Jarvis ED, O'Brien SJ, Antunes A.

BMC Genomics. 2015 Oct 6;16:751. doi: 10.1186/s12864-015-1924-3.


Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED.

Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1578.


Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.

Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MT, Jarvis ED, O'Brien SJ, Johnson WE, Antunes A.

Mol Biol Evol. 2015 Nov;32(11):2832-43. doi: 10.1093/molbev/msv155. Epub 2015 Jul 28.


A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis.

Ribeiro ÂM, Zepeda-Mendoza ML, Bertelsen MF, Kristensen AT, Jarvis ED, Gilbert MT, da Fonseca RR.

BMC Evol Biol. 2015 Jun 30;15:124. doi: 10.1186/s12862-015-0409-y.


Core and Shell Song Systems Unique to the Parrot Brain.

Chakraborty M, Walløe S, Nedergaard S, Fridel EE, Dabelsteen T, Pakkenberg B, Bertelsen MF, Dorrestein GM, Brauth SE, Durand SE, Jarvis ED.

PLoS One. 2015 Jun 24;10(6):e0118496. doi: 10.1371/journal.pone.0118496. eCollection 2015.


Genomics: Bird sequencing project takes off.

Zhang G, Rahbek C, Graves GR, Lei F, Jarvis ED, Gilbert MT.

Nature. 2015 Jun 4;522(7554):34. doi: 10.1038/522034d. No abstract available.


Male mice song syntax depends on social contexts and influences female preferences.

Chabout J, Sarkar A, Dunson DB, Jarvis ED.

Front Behav Neurosci. 2015 Apr 1;9:76. doi: 10.3389/fnbeh.2015.00076. eCollection 2015.


Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.


Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SY, Burt DW, Ponting CP, Jarvis ED, Gilbert MT, Yang H, Wang J, Lambert DM, Wang J, Zhang G.

Gigascience. 2014 Dec 12;3(1):27. doi: 10.1186/2047-217X-3-27. eCollection 2014.


Comparative genomic data of the Avian Phylogenomics Project.

Zhang G, Li B, Li C, Gilbert MT, Jarvis ED, Wang J; Avian Genome Consortium.

Gigascience. 2014 Dec 11;3(1):26. doi: 10.1186/2047-217X-3-26. eCollection 2014.


Maintenance and neuronal differentiation of chicken induced pluripotent stem-like cells.

Dai R, Rossello R, Chen CC, Kessler J, Davison I, Hochgeschwender U, Jarvis ED.

Stem Cells Int. 2014;2014:182737. doi: 10.1155/2014/182737. Epub 2014 Dec 9.


Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.

Pereira J, Johnson WE, O'Brien SJ, Jarvis ED, Zhang G, Gilbert MT, Vasconcelos V, Antunes A.

PLoS One. 2014 Dec 30;9(12):e74132. doi: 10.1371/journal.pone.0074132. eCollection 2014.


The basal ganglia within a cognitive system in birds and mammals.

Petkov CI, Jarvis ED.

Behav Brain Sci. 2014 Dec;37(6):568-9; discussion 577-604. doi: 10.1017/S0140525X13004160.


Convergent transcriptional specializations in the brains of humans and song-learning birds.

Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256846. doi: 10.1126/science.1256846.


Core and region-enriched networks of behaviorally regulated genes and the singing genome.

Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256780. doi: 10.1126/science.1256780.


Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.


Evidence for a single loss of mineralized teeth in the common avian ancestor.

Meredith RW, Zhang G, Gilbert MT, Jarvis ED, Springer MS.

Science. 2014 Dec 12;346(6215):1254390. doi: 10.1126/science.1254390. Epub 2014 Dec 11.


Complex evolutionary trajectories of sex chromosomes across bird taxa.

Zhou Q, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1246338. doi: 10.1126/science.1246338. Epub 2014 Dec 11.


Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.


Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.


Avian genomes. A flock of genomes. Introduction.

Zhang G, Jarvis ED, Gilbert MT.

Science. 2014 Dec 12;346(6215):1308-9. doi: 10.1126/science.346.6215.1308. No abstract available.


Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species.

Li S, Li B, Cheng C, Xiong Z, Liu Q, Lai J, Carey HV, Zhang Q, Zheng H, Wei S, Zhang H, Chang L, Liu S, Zhang S, Yu B, Zeng X, Hou Y, Nie W, Guo Y, Chen T, Han J, Wang J, Wang J, Chen C, Liu J, Stambrook PJ, Xu M, Zhang G, Gilbert MT, Yang H, Jarvis ED, Yu J, Yan J.

Genome Biol. 2014;15(12):557.


Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK.

BMC Genomics. 2014 Dec 11;15:1060. doi: 10.1186/1471-2164-15-1060.


Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.

Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H.

Genome Biol. 2014;15(12):549.


Low frequency of paleoviral infiltration across the avian phylogeny.

Cui J, Zhao W, Huang Z, Jarvis ED, Gilbert MT, Walker PJ, Holmes EC, Zhang G.

Genome Biol. 2014;15(12):539.


Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles.

Greenwold MJ, Bao W, Jarvis ED, Hu H, Li C, Gilbert MT, Zhang G, Sawyer RH.

BMC Evol Biol. 2014 Dec 12;14:249. doi: 10.1186/s12862-014-0249-1.


Genomic resources for the endangered Hawaiian honeycreepers.

Callicrate T, Dikow R, Thomas JW, Mullikin JC, Jarvis ED, Fleischer RC; NISC Comparative Sequencing Program.

BMC Genomics. 2014 Dec 12;15:1098. doi: 10.1186/1471-2164-15-1098.

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